Personal tools

Coexpression cluster:C297

From FANTOM5_SSTAR

Revision as of 05:38, 19 October 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C297_Eosinophils_CD4_Basophils_Natural_Neutrophils_CD8_Peripheral



Phase1 CAGE Peaks

  Short description
Hg19::chr10:35416142..35416169,+ p3@CREM
Hg19::chr10:35416172..35416184,+ p13@CREM
Hg19::chr11:3862855..3862867,+ p@chr11:3862855..3862867
+
Hg19::chr12:106697097..106697117,- p@chr12:106697097..106697117
-
Hg19::chr14:52314051..52314062,- p@chr14:52314051..52314062
-
Hg19::chr17:38497640..38497647,+ p27@RARA
Hg19::chr17:62097904..62097915,- p4@ICAM2
Hg19::chr17:76837188..76837205,+ p@chr17:76837188..76837205
+
Hg19::chr19:41769066..41769091,+ p@chr19:41769066..41769091
+
Hg19::chr19:59085102..59085126,+ p@chr19:59085102..59085126
+
Hg19::chr1:185536411..185536432,+ p@chr1:185536411..185536432
+
Hg19::chr1:198650975..198650986,- p@chr1:198650975..198650986
-
Hg19::chr1:198651031..198651051,- -
p@chr1:198651031..198651051
Hg19::chr1:198651180..198651193,+ p@chr1:198651180..198651193
+
Hg19::chr1:198651195..198651213,+ p@chr1:198651195..198651213
+
Hg19::chr1:45273151..45273188,+ p@chr1:45273151..45273188
+
Hg19::chr20:34356239..34356262,+ p@chr20:34356239..34356262
+
Hg19::chr20:42839727..42839752,+ p1@LOC100505783
Hg19::chr20:43150543..43150551,- p@chr20:43150543..43150551
-
Hg19::chr20:43150846..43150896,+ p@chr20:43150846..43150896
+
Hg19::chr20:43150918..43150934,+ p@chr20:43150918..43150934
+
Hg19::chr20:5590658..5590681,+ p@chr20:5590658..5590681
+
Hg19::chr22:39097139..39097148,+ p@chr22:39097139..39097148
+
Hg19::chr22:47158371..47158384,- p@chr22:47158371..47158384
-
Hg19::chr2:170441202..170441230,- p@chr2:170441202..170441230
-
Hg19::chr2:197034975..197035000,- p@chr2:197034975..197035000
-
Hg19::chr2:197035024..197035040,- p@chr2:197035024..197035040
-
Hg19::chr2:55845186..55845202,+ p@chr2:55845186..55845202
+
Hg19::chr2:97204412..97204438,- p@chr2:97204412..97204438
-
Hg19::chr4:152020461..152020473,- p@chr4:152020461..152020473
-
Hg19::chr6:108145154..108145165,- p@chr6:108145154..108145165
-
Hg19::chr7:36816762..36816783,- p@chr7:36816762..36816783
-
Hg19::chr7:66146955..66146980,- -
p@chr7:66146955..66146980
Hg19::chr7:66309834..66309894,- p1@LOC729156
Hg19::chr7:75796016..75796041,+ p@chr7:75796016..75796041
+
Hg19::chr8:118532766..118532792,- p@chr8:118532766..118532792
-
Hg19::chr8:64080945..64080978,- p@chr8:64080945..64080978
-
Hg19::chr9:100684655..100684671,+ p@chr9:100684655..100684671
+
Hg19::chr9:132650707..132650725,- p8@FNBP1
Hg19::chr9:132650755..132650788,- p4@FNBP1
Hg19::chr9:132650792..132650809,- p12@FNBP1
Hg19::chr9:33159824..33159848,+ p@chr9:33159824..33159848
+


Enriched pathways on this co-expression clusterSummary:
Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.
Analyst: Emmanuel Dimont

link to source dataset
data


p.valueFDRnGenesnPathwayName
6.41827216562196e-050.040627662808387273Notch up reg. targets (Netpath):NetPath_3



Enriched Gene Ontology terms on this co-expression clusterSummary: Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter.
Analyst: Erik Arner

link to source dataset
data


GO IDGO nameFDR corrected p-value
GO:0003713transcription coactivator activity0.0112437650335631
GO:0008140cAMP response element binding protein binding0.0112437650335631
GO:0003712transcription cofactor activity0.0112437650335631
GO:0016563transcription activator activity0.0112437650335631
GO:0008134transcription factor binding0.0175123136485932
GO:0003708retinoic acid receptor activity0.0378801066558398



Enriched sample ontology terms on this co-expression clusterSummary:To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data


Cell Type
Ontology termp-valuen
leukocyte2.77e-92136
hematopoietic stem cell5.88e-76168
angioblastic mesenchymal cell5.88e-76168
nongranular leukocyte7.76e-72115
hematopoietic lineage restricted progenitor cell1.36e-71120
hematopoietic cell1.32e-70177
hematopoietic oligopotent progenitor cell1.85e-67161
hematopoietic multipotent progenitor cell1.85e-67161
classical monocyte5.30e-5142
CD14-positive, CD16-negative classical monocyte5.30e-5142
myeloid leukocyte7.92e-4772
defensive cell6.82e-4348
phagocyte6.82e-4348
granulocyte monocyte progenitor cell6.76e-3767
macrophage dendritic cell progenitor1.69e-3561
myeloid lineage restricted progenitor cell5.02e-3466
monopoietic cell2.36e-3359
monocyte2.36e-3359
monoblast2.36e-3359
promonocyte2.36e-3359
myeloid cell3.20e-33108
common myeloid progenitor3.20e-33108
lymphoid lineage restricted progenitor cell1.24e-3252
lymphocyte8.83e-3253
common lymphoid progenitor8.83e-3253
nucleate cell3.58e-3055
mature alpha-beta T cell3.14e-2318
alpha-beta T cell3.14e-2318
immature T cell3.14e-2318
mature T cell3.14e-2318
immature alpha-beta T cell3.14e-2318
mesenchymal cell6.09e-21354
connective tissue cell5.34e-20361
T cell8.52e-1925
pro-T cell8.52e-1925
stuff accumulating cell7.50e-1887
motile cell1.05e-16386
CD8-positive, alpha-beta T cell2.32e-1511
intermediate monocyte2.95e-149
CD14-positive, CD16-positive monocyte2.95e-149
granulocyte3.23e-148
multi fate stem cell9.53e-13427
stem cell1.07e-12441
somatic stem cell3.29e-12433
CD4-positive, alpha-beta T cell2.83e-116
lymphocyte of B lineage2.91e-1124
pro-B cell2.91e-1124
B cell6.37e-1114
blood cell8.86e-1011
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.01e-3898
blood island1.01e-3898
hemolymphoid system1.03e-34108
bone marrow1.65e-3276
immune system9.55e-3293
bone element4.67e-2982
skeletal element3.46e-2590
skeletal system3.01e-21100
connective tissue1.02e-18371
lateral plate mesoderm1.37e-10203
musculoskeletal system1.21e-07167


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary:The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysisSummary: For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained.
Analyst: Erik Arner

link to source dataset

data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
ATF3#46784.278699909715950.0004663231207055730.00429170958788943
BATF#10538105.799476617215155.93965793861152e-060.00017815391598238
BCL11A#53335117.430095384278041.60966870389735e-078.91368980733483e-06
BCL3#60254.112750333778370.007083034499878040.0295389945347108
BCLAF1#9774147.217549203373953.07699218625634e-092.57292223331005e-07
BRCA1#672178.169807641304864.96860992546389e-126.49457637053221e-10
BRF2#552904102.3405315614627.88423726816163e-084.71874989140133e-06
CCNT2#905172.564653019246780.0001085459125704390.00151071782555226
CEBPB#1051203.79578458372612.93067916697899e-081.99269011406327e-06
CHD2#1106133.201721353417120.0001096654379979560.0015250797175857
CTCF#10664172.169627579577990.000844294016354890.00636658648188364
CTCFL#140690104.701541514041513.63874760731806e-050.000704145194294406
E2F4#187492.714584353275240.004824661988887480.0226382816720918
E2F6#1876192.269665688148820.0001824568162161910.00221011452433342
EBF1#1879173.604998485516031.11799004160593e-064.60417042410418e-05
EGR1#1958252.969154223101272.39834497378206e-081.68673906206616e-06
ELF1#1997272.737348687804852.16864782773001e-081.53657673324488e-06
ELK4#2005124.638766188133725.72957160997209e-060.000172397213878961
EP300#2033182.903117882667091.07598646932828e-050.000279053764266642
ETS1#2113153.474557472215129.80106808828958e-060.000257189384440421
FOS#2353132.785081405133980.0004405220379280360.00410416423899787
FOSL2#2355135.240300187126245.30749507015305e-072.47459588228444e-05
FOXA1#3169133.429963255762165.39654083920658e-050.000914950208938143
GABPB1#2553213.533841918091093.76526773060242e-082.4951827190126e-06
GATA1#262392.905780316528670.003069829661269730.0161826135671992
GTF2B#295986.084539035109384.18112365998534e-050.000757585659134645
GTF2F1#2962144.246553625585882.13268969595545e-067.75813232866217e-05
HEY1#23462282.693407362070471.22115425605082e-089.09024442962877e-07
HMGN3#9324163.115637227943081.76253764855585e-050.000402443527497866
IRF1#3659152.727558483415680.0001686044960766620.00206120624672252
IRF4#3662136.78306345065892.69676201628614e-081.85538292634327e-06
JUND#3727182.997713117944736.81826711745991e-060.000198188978424825
MAX#4149203.072645480479589.91561689780469e-074.20282919314052e-05
MEF2A#4205125.355208831326871.29637386153801e-065.15190219654369e-05
MEF2C#420898.85243310556236.12772843712137e-072.81183580951019e-05
MXI1#4601194.506425260629214.80064081371731e-093.87161487215306e-07
MYC#4609253.108501114053229.1160011331437e-096.96463820295826e-07
NFKB1#4790283.658708949462566.95021977783518e-128.85212199240645e-10
NFYB#480183.192341572102180.003041821609101670.0160471186054943
NRF1#489992.616488453080910.006131293458304640.0271091891745429
PAX5#5079264.12877866215775.12966171779913e-126.68000922874343e-10
PBX3#509094.695967004302319.65983251816607e-050.00137503509385954
POLR2A#5430402.045193501483881.34958418921476e-111.66213706529953e-09
POU2F2#5452214.553062028871263.75602121697042e-103.73595333218261e-08
RAD21#5885122.958581112987520.0004535969171531480.0042173247067175
REST#5978112.527388473271620.002986984463435450.0158797490647358
RFX5#5993236.597665452987791.26053327826328e-142.1688440699924e-12
RXRA#625694.301703672671410.0001872675035127390.0022647094487456
SIN3A#25942303.863489090582241.04916321365618e-131.64032270765026e-11
SIX5#14791272.84778589257650.01038085244441590.0385440076949073
SMC3#9126113.940339554625276.90500969681743e-050.00110099588965789
SP1#6667283.79892091876062.70412291122094e-123.63469617406698e-10
SP2#666874.35892174897410.0009897172147747680.00710412894803175
SPI1#6688224.297502790178573.34981793693828e-103.3639580338067e-08
SRF#6722206.570084886746581.69092484396929e-122.32366447078038e-10
STAT1#677273.451097916199870.003716320439153190.0187411294227291
STAT3#6774133.256024880071559.23444819976633e-050.00134378784385592
TAF1#6872342.706275564650951.14184188233196e-111.42306472970009e-09
TAF7#6879112.994375320337220.0007547943065901110.00593554420495178
TBP#6908343.000719127649464.66216504574772e-136.82905827788002e-11
TCF12#6938215.317232451093212.04337792876457e-112.45296951152003e-09
TCF7L2#6934123.077193303753530.000316052753437910.00323832370414029
USF1#7391142.120499759069320.003707991434821470.0187018359714743
USF2#7392103.093380329778470.001079963216966110.00762354027825098
YY1#7528222.572518011828214.28712985869587e-060.000135638762590833
ZEB1#693583.216844193817880.002901896662633210.0156820441658258
ZNF263#10127122.349097610574480.003410825010177240.0173826747298053



Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data